Constructor Detail

• Taxonomy

  public Taxonomy()

Method Detail

• asSimpleText

  public java.lang.StringBuffer asSimpleText()

  Specified by:

  asSimpleText in interface PhylogenyData

• getUri

  public Uri getUri(int index)

  Specified by:

  getUri in interface MultipleUris

• addUri

  public void addUri(Uri uri)

  Specified by:

  addUri in interface MultipleUris

• asText

  public java.lang.StringBuffer asText()

  Specified by:

  asText in interface PhylogenyData

• copy

  public PhylogenyData copy()

  Description copied from interface: PhylogenyData
  Creates a new PhylogenyData object with identical values as this PhylogenyData. This ~should~ return a deep copy, but not there yet.

  Specified by:

  copy in interface PhylogenyData

  Returns:

  a ~deep~ copy of this PhylogenyData

• equals

  public boolean equals(java.lang.Object o)

  Overrides:

  equals in class java.lang.Object

• getAuthority

  public java.lang.String getAuthority()

• getCommonName

  public java.lang.String getCommonName()

• getIdentifier

  public Identifier getIdentifier()

• getRank

  public java.lang.String getRank()

• getScientificName

  public java.lang.String getScientificName()

• getSynonyms

  public java.util.List<java.lang.String> getSynonyms()

• getTaxonomyCode

  public java.lang.String getTaxonomyCode()

• getUris

  public java.util.List<Uri> getUris()

  Specified by:

  getUris in interface MultipleUris

• hashCode

  public int hashCode()

  Overrides:

  hashCode in class java.lang.Object

• init

  public void init()

• isEmpty

  public boolean isEmpty()

• isEqual

  public boolean isEqual(PhylogenyData data)

  If this and taxonomy 'data' has an identifier, comparison will be based on that. Otherwise, if this and taxonomy 'data' has a code, comparison will be based on that. Otherwise, if Taxonomy 'data' has a scientific name, comparison will be based on that (case insensitive!). Otherwise, if Taxonomy 'data' has a common name, comparison will be based on that (case insensitive!). (Note. This is important and should not be change without a very good reason.)

  Specified by:

  isEqual in interface PhylogenyData

  Returns:

  in general, true if and only if all fiels are exactly identical, false otherwise

• setAuthority

  public void setAuthority(java.lang.String authority)

• setCommonName

  public void setCommonName(java.lang.String common_name)

• setIdentifier

  public void setIdentifier(Identifier identifier)

• setRank

  public void setRank(java.lang.String rank)
               throws PhyloXmlDataFormatException

  Throws:

  PhyloXmlDataFormatException

• setScientificName

  public void setScientificName(java.lang.String scientific_name)

• setTaxonomyCode

  public void setTaxonomyCode(java.lang.String taxonomy_code)
                       throws PhyloXmlDataFormatException

  Throws:

  PhyloXmlDataFormatException

• setUris

  public void setUris(java.util.List<Uri> uris)

  Specified by:

  setUris in interface MultipleUris

• toNHX

  public java.lang.StringBuffer toNHX()

  Specified by:

  toNHX in interface PhylogenyData

• toPhyloXML

  public void toPhyloXML(java.io.Writer writer,
                         int level,
                         java.lang.String indentation)
                  throws java.io.IOException

  Description copied from interface: PhylogenyData
  Writes a phyloXML representation of this phylogeny data.

  Specified by:

  toPhyloXML in interface PhylogenyData

  Throws:

  java.io.IOException

• toString

  public java.lang.String toString()

  Overrides:

  toString in class java.lang.Object

• compareTo

  public int compareTo(Taxonomy o)

  Specified by:

  compareTo in interface java.lang.Comparable<Taxonomy>

• setLineage

  public void setLineage(java.util.List<java.lang.String> lineage)

• getLineage

  public java.util.List<java.lang.String> getLineage()